Is ribosome synthesis controlled by pol I transcription?
Stéphane Chédin, Arnaud Laferté, Tran Hoang, Denis L J Lafontaine, Michel
Riva, Christophe Carles
To cite this version:
Stéphane Chédin, Arnaud Laferté, Tran Hoang, Denis L J Lafontaine, Michel Riva, et al.. Is
ribosome synthesis controlled by pol I transcription?. Cell Cycle, Taylor & Francis, 2007, 6 (1),
pp.11-5.
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[Cell Cycle 6:1, 11-15, 1 January 2007]; ©2007 Landes Bioscience
Extra View
Is Ribosome Synthesis Controlled by Pol I Transcription?
Stéphane Chédin1
Arnaud Laferté1
Tran Hoang2
Denis L.J. Lafontaine2
Michel Riva1,*
Christophe Carles1
Abstract
National de la Recherche Scientifique; Université Libre de Bruxelles;
Institut de Biologie et de Médecine Moléculaires; Charleroi-Gosselies, Belgique
*Correspondence to: Michel Riva; CEA; Laboratoire Régulation de l’Expression des
Gènes et Epigénétique; Service de Biologie Integrative et Génétique Moléculaire;
Gif sur Yvette, France; Tel.: +33.16.908.8417; Fax: +33.16.908.4712; Email:
[email protected]
Cellular growth and division is tightly regulated by ribosome synthesis, a major cellular
undertaking that is energetically very costly (reviewed in refs. 2 and 3). A striking feature
of ribosome synthesis is a requirement for the coordinated activity of the three forms of
RNA polymerase to produce the building blocks for ribosome construction. Pol I synthesizes the 35S rRNA which is processed into mature 25S, 18S and 5.8S rRNAs; Pol II
synthesizes the mRNAs encoding the ribosomal proteins (RPs); and Pol III synthesizes 5S
rRNA. How in this process coordination between the three forms of RNA polymerase is
achieved is still unclear.
Recently, we showed in yeast that the accumulation of large ribosomal RNAs, as a
result of deregulated Pol I transcription, led to the concomitant accumulation of 5S
rRNA, of mRNAs encoding RPs, and of fully assembled ribosomes.1 This observation
points to a central role for Pol I activity in ribosome synthesis and suggests that Pol I
transcription integrates the coordinated regulation of the two other forms of nuclear RNA
polymerase.
.D
Original manuscript submitted: 11/09/06
Manuscript accepted: 11/09/06
IST
2Fonds
OT
D
Régulation de l’Expression des Gènes et Epigénétique; Service
de Biologie Integrative et Génétique Moléculaire; Gif sur Yvette, France
ON
1CEA; Laboratoire
RIB
UT
E
.
Regulation of growth ultimately depends on the control of synthesis of new ribosomes.
Ribosome biogenesis is thus a key element of cell biology, which is tightly regulated in
response to environmental conditions. In eukaryotic cells, the supply of ribosomal components involves the activities of the three forms of nuclear RNA polymerase (Pol I, Pol II and
Pol III). Recently, we demonstrated that upon rapamycin treatment, a partial derepression
of Pol I transcription led to a concomitant derepression of Pol II transcription restricted to
a small subset of class II genes encompassing the genes encoding all ribosomal proteins,
and 19 additional genes.1 The products of 14 of these 19 genes are principally involved
in rDNA structure, ribosome biogenesis or translation, whereas the five remaining genes
code for hypothetical proteins. We demonstrate that the proteins encoded by these five
genes are required for optimal pre-rRNA processing. In addition, we show that cells in
which regulation of Pol I transcription was specifically impaired are either resistant or
hypersensitive to different stresses compared to wild‑type cells. These results highlight the
critical role of the regulation of Pol I activity for the physiology of the cells.
CE
Previously published online as a Cell Cycle E-publication:
http://www.landesbioscience.com/journals/cc/abstract.php?id=3593
IEN
Key words
SC
yeast, transcription, Pol I, Pol II, ribosome
synthesis, rapamycin, co-regulation
BIO
Acknowledgements
©
20
06
LA
ND
ES
We thank C. Mann for a critical reading of
the manuscript. A.L. is a recipient of a grant
from the MENRT delivered by Paris-VII
University. Research in the Lab of D.L.J.L.
was supported by the Fonds National de
la Recherche Scientifique, Université Libre
de Bruxelles, Communauté Française de
Belgique (ARC Convention N°06/11-345),
Fonds Alice & David van Buuren, Fonds
Brachet, Fonds Defay, Fonds Lewin-Inès de
Castro, Fonds Hoguet, Fonds Xénophilia and
International Brachet Stiftüng.
www.landesbioscience.com
The CARA strain, or How to Make Pol I Transcription Constitutive?
In yeast, Pol I transcription initiation requires four general transcription factors: the
upstream activating factor (UAF), the core factor (CF), the TATA binding protein (TBP)
and the monomeric factor Rrn3. The two multimeric complexes UAF and CF bind to the
rDNA promoter in conjonction with TBP to form the class I preinitiation complex,4‑6
whereas establishment of a transcription‑competent initiation complex requires the interaction of Rrn3 with both Pol I and promoter‑bound factors.7,8 The essential and reversible
interaction of the enzyme with Rrn3 is a critical event for Pol I transcription (reviewed
in refs. 9–11), and has been shown to be a prime target for the regulation of the Pol I
activity.8,12,13 To interfere with these mechanisms, we constructed a yeast strain, named
CARA (for Constitutive Association of Rrn3 and A43), in which the endogenous, essential
Rrn3 factor and the A43 subunit of the Pol I that interacts with Rrn3,14 were supplied as
an Rrn3‑A43 fusion protein.1 The chimeric construct assembled properly within Pol I and
formed a constitutively active, non dissociable Pol I‑Rrn3 complex. Remarkably, under
standard growth conditions, the CARA strain was not affected for growth and microarray
analysis revealed that CARA cells have an mRNA expression profile indistinguishable from
that of wild‑type cells (Fig. 1, no rapamycin).
Cell Cycle
11
Pol I and Ribosome Biogenesis
Ribosome synthesis is tightly regulated in response to a wide
variety of intra and extra cellular stimuli.2,15,16 In particular,
the evolutionarily conserved TOR (target of rapamycin) signaling
pathway regulates ribosome biogenesis and protein synthesis (in
addition to nutrient import, autophagy and cell cycle progression).
The TOR pathway is specifically inhibited by the antifungal and
anticancer drug rapamycin. Upon rapamycin treatment, the level of
all transcripts analyzed in our microarray experiments was similarly
regulated in wild‑type and CARA cells, with the notable exception of
147 mRNAs that were significantly over‑represented in CARA cells
(Fig. 1 and ref. 1). Remarkably, these account for only 2.5% of all the
mRNAs analyzed. This striking observation demonstrates that upon
rapamycin treatment, deregulation of Pol I transcription leads to a
selective and concomitant deregulation of a highly specific subset of
class II transcripts. The genes encoding these mRNAs can be grouped
in four classes (see Table 1 for a summary):
(1) Group A represents the vast majority (128 of 147) of the
genes specifically deregulated in CARA cells and encompasses the
RP genes. Among the 138 RP genes of the yeast S. cerevisiae, 131 are
represented on the DNA array used in the experiment. Surprisingly,
the level of only 3 RP mRNAs is similar in CARA and wild‑type cells
upon rapamycin treatment (Fig. 1). Each of the corresponding genes
(RPL1A, RPL7B and RPL33A) belongs to a related pair, a general
feature in S. cerevisiae that has retained many of the duplicated RP
genes that were generated following the ancestral whole genome
duplication.17 In the experiment depicted in Figure 1, the level of
mRNAs of the other member of each gene pair (namely RPL1B,
RPL7A and RPL33B) however, was significantly overrepresented in
CARA cells. Since for each pair of RP genes, the two corresponding
mRNAs have a near identical nucleotide sequence and thus cannot
be easily distinguished on the microarray, these data suggest that
the absence of a specific rapamycin‑dependent deregulation of the
RPL1A, RPL7B and RPL33A genes in the CARA cells in fact likely
reflects technical limitations.
(2) Group B (see Table 1) includes eight genes whose products
are involved in ribosome synthesis, assembly and/or function: Utp22
is involved in the 35S primary transcript processing,18 Emg1 is
required for the maturation of the 18S rRNA and for 40S ribosome
production,19 Stm1 directly binds to mature 80S ribosomes and
polysomes,20 Rpg1 is a translation initiation factor,21 Asc1 acts
as a negative regulator of translation,22 and Cdc60 aminoacylates
leucyl‑tRNA.23 Finally, SDC1 and SPP1, whose products are two
subunits of the COMPASS (Set1C) complex which methylates lysine
4 of histone H3, and which is involved in rDNA silencing,24,25 are
also specifically deregulated in CARA cells during the rapamycin
treatment.
(3) Group C (see Table 1) contains six genes encoding proteins
whose function is apparently unrelated to cytoplasmic ribosome
or translation. LEA1 codes for a component of U2 snRNP.26 Gip2
is a putative regulatory subunit of the protein phosphatase Glc7p,
involved in glycogen metabolism.27 FET3 encodes an integral
membrane multicopper oxidase, which mediates resistance to copper
ion toxicity.28,29 BEM4 codes for a protein involved both in the establishment of cell polarity and bud emergence, in Rho protein signal
transduction,30 and in maintenance of proper telomere length.31
Finally, the products of the last two genes are involved in mitochondrial metabolism: CBP3 encodes a mitochondrial chaperone required
for assembly of the cytochrome bc1 complex32,33 whereas MRLP24
codes for a mitochondrial RP of the large subunit.34
(4) The last class of genes (group D) encompasses five non-essential genes encoding hypothetical proteins (YDR445C, YER039C‑A,
12
Figure 1. Members of the Ribi regulon are not deregulated in the CARA strain
upon rapamycin treatment. Wild‑type (WT) and CARA cells were grown in
complete medium to OD600 = 1 (mid‑log phase) and further incubated for
60 min with rapamycin or without rapamycin (inset). Cells were harvested
and total RNAs were extracted. RNAs (20 mg) were labeled by reverse transcription in the presence of Cy5 dUTP (WT) or Cy3 dUTP (CARA) and used
to probe a microarray harboring all yeast ORFs. Results were analyzed using
the GeneSpring software (Silicon Genetics). A scatterplot representation of
expression levels is displayed. Each individual spot corresponds to a gene,
and its location on the diagonal indicates that the abundance of the corresponding mRNA is similar in both strains. mRNAs encoding RP (black spots)
are present at the same level in untreated WT and CARA cells (inset) but
are specifically overrepresented in CARA cells in the presence of rapamycin
(from a threefold to a 13‑fold factor, with an average factor of 7.7). In sharp
contrast, after rapamycin treatment, the abundance of mRNAs from the Ribi
regulon (pink spots) remains identical in both WT and CARA strain. The two
spots, corresponding to RRN3 and RPA43 mRNAs (indicated by an arrow),
which belongs to the Ribi regulon, are overexpressed in CARA cells because
the Rrn3‑A43 fusion is expressed from a multicopy plasmid.
YOL047C, YOL048C and YPL216W, see Table 1). To test whether
these proteins are involved in ribosome synthesis, the pre-rRNA
processing pathway was characterized by Northern blot hybridization in yeast strains deleted for each of these five genes (Fig. 2). All
five strains analyzed were defective for pre-rRNA processing. The
pathway leading to the synthesis of the small ribosomal subunit
rRNA (18S rRNA) was most affected (cleavages at sites A0‑A2). Since
the aberrant 23S RNA that extends from the transcription start site
to site A3 was not detected in any of the strains tested, we concluded
that cleavages at sites A0‑A2 are delayed to various extent and that all
five genes of class D are required for optimal pre-rRNA processing.
Altogether, our microarray analysis underscores a very high
specificity for the 147 mRNAs distinctively deregulated in CARA
cells upon rapamycin treatment. The most prominent observation
concerns the RP genes (group A). Although spread throughout the
yeast genome, these genes are arguably the most coordinately regulated cluster of genes and are thus considered as a regulon (i.e., the RP
regulon).2,16,35 Remarkably, however, regulation of another regulon,
the Ribi regulon (for ribosome biogenesis), which shows nearly
identical transcriptional responses as RP genes to environmental or
genetic perturbations,16,36‑39 is similar in CARA and wild‑type cells
upon rapamycin treatment (Fig. 1). The Ribi regulon encompasses
a large number of genes (>200) encoding proteins involved in ribosome biogenesis, a complex process implicating accessory factors that
Cell Cycle
2007; Vol. 6 Issue 1
Pol I and Ribosome Biogenesis
Table 1
Class II transcripts deregulated in CARA cells upon rapamycin treatmenta
CARA / WT b
GroupNumber of Genes
Systematic Name Common Name
No Rapamycin
+ Rapamycin
Biological Process c
RPs
1.0d
7.7d
RPG1�
0.9
5.5
YDR469W
SDC1
1.0
5.0
YGR090W
UTP22
0.7
3.6
rDNA structure, ribosome
YLR150W
STM1
0.9
3.7
biogenesis or translation
YLR186W
EMG1
0.9
4.5
YMR116C
ASC1
0.9
4.3
YPL160W
CDC60
0.7
6.0
YPL138C
SPP1
1.0
3.9
C
GIP2
1.1
3.3
YMR058W
FET3
1.1
3.0
YMR193W
MRPL24
1.0
4.4
Function unrelated
YPL161C
BEM4
0.9
6.0
to ribosome biogenesis
YPL213W
LEA1
0.9
3.4
YPL215W
CBP3
1.1
9.4
‑
1.0
3.2
YER039C‑A
‑
0.9
3.4
YOL047C
‑
1.0
5.2
YOL048C
‑
0.9
3.9
‑
1.1
9.0
A
128
B���
��
8YBR079C
��������
D
6YER054C
5YDR445C
��������
YPL216W
Ribosome Components
Uncharacterized function
aGenes specifically over‑represented (>= 3‑fold increase) in CARA cells versus WT cells in the presence of rapamycin. bRatio of expression in CARA cells over WT cells. cAccording to the Saccharomyces Genome Database
available at http://www.yeastgenome.org. dAverage for the 128 RP genes (for details, see ref. 1)
assemble and modify rRNA and RPs36‑38,40 as well as additional
functional categories including subunits of Pol I and Pol III, enzymes
involved in ribonucleotide metabolism, tRNA synthetases, and
translation factors.16,37,38 The Ribi regulon thus consists of non-RP
genes that enhance translational capacity.
In conclusion, the observation that the deregulation of Pol I
activity specifically affects transcription of the RP regulon but not
that of the Ribi regulon (Fig. 1) emphasizes the very high specificity
of the cross‑talk existing between the Pol I and Pol II transcriptional
machineries.
What are the Consequences of Ribosome Biogenesis
Deregulation?
Genome‑wide analyses have clearly documented that most environmental alterations trigger important modifications of the yeast
transcriptome. In particular, under stressful conditions, genes related
to the ESR (Environmental Stress Response) exhibit either of two
opposite responses: a cluster of around 600 genes, including all RP
genes, is repressed, whereas a second cluster of approximately 300
genes is induced.16 Even if Pol I and Pol III transcriptional activities
were not the central focus of these systematic analyses, they are down
regulated by most of the environmental stresses.41‑45 Altogether,
these studies indicate that the concomitant down regulation of the
synthesis of all ribosomal components is a general feature of yeast
physiology in response to environmental changes. Since ribosome
biogenesis is one of the most energy consuming cellular process,3 it is
tempting to attribute this phenomenon to a cellular “energy‑saving”
strategy but other explanations can be considered. For instance, it
www.landesbioscience.com
has been shown that signal‑induced changes in the transcriptome are
amplified at the translational level.46 This effect, named potentiation,
is characterized by a more efficient translation of mRNAs encoding
genes that are induced in the transcriptome, and by lower translation efficiency for mRNAs encoding genes that are down regulated.
Therefore, to modify rapidly the protein content of cells, one can
imagine that a down regulation of ribosome biogenesis is required,
while modifying the transcriptome profile. Little is known, however,
on the effect on cell physiology of a deregulation of ribosome
synthesis under stress conditions.
Taking advantage of the properties of the CARA strain, we investigated the effect of deregulating ribosome biogenesis in the presence
of rapamycin.
In the absence of stress, we did not detect any growth differences
between CARA and wild‑type cells in complete medium (YPD),
either liquid1 or solid (Fig. 3A). In contrast, CARA cells were hypersensitive to rapamycin in plate assays for all drug concentrations
tested (from 0.05 mg/ml to 1.6 mg/ml, Fig. 3B and data not shown).
This hypersensitivity to rapamycin was observed for cells spotted
from log‑phase or from post‑diauxic cultures (Fig. 3B). This result
indicates that interfering with the rapamycin‑dependent transcriptional repression of ribosomal components is deleterious for cell
growth.
Next, we investigated how CARA cells responded to hydrogen
peroxide, which, in contrary to rapamycin, induces a transient
modification of the expression pattern of the ESR genes.16,47
Wild‑type and CARA cells, from either log‑phase or post‑diauxic
culture, were spotted on plates containing different concentration
of hydrogen peroxide. Wild‑type and CARA cells from log‑phase
Cell Cycle
13
Pol I and Ribosome Biogenesis
Figure 2. Group D genes are required for ribosomes synthesis. (A) Cells
deleted for each of the five genes listed in Group D were grown to early
log phase in complete medium. Total RNAs were extracted, separated by
electrophoresis on denaturing 1.2% agarose/formaldehyde (panels a–g)
or acrylamide gels (panels h and i), transferred to nylon membranes and
analyzed by Northen‑blot hybridization. RNA species detected to the right.
The 18S rRNA to 25S rRNA ratio was established using Phosphor Imager
quantitation (Typhoon and Image Quant, GE Healthcare). Oligonucleotides
used in the hybridizations are as described in reference 52. (B) Schematic
representation of the structure of the 35S rRNA primary Pol I transcript. The
coding sequences for three out of the four mature rRNAs (25S, 18S, and
5.8S) are embedded within external (5'‑ and 3'‑ETS) and internal (ITS1 and
ITS2) transcribed spacer. Cleavage sites A0 to E are indicated. +1, transcription start site. The fourth rRNA (5S) is independently transcribed by Pol III
(not represented). For a full description of the pre-rRNA processing pathway,
(see ref. 53).
cultures exhibited the same sensitivity to hydrogen peroxide (Fig. 3C
and D). Surprisingly, CARA cells were significantly more resistant to
hydrogen peroxide compared to wild‑type cells when spotted from
post‑diauxic cultures (Fig. 3C and D). The reasons why post‑diauxic
culture cells show a greater resistance to hydrogen peroxide when
containing a larger amount of assembled ribosome1 are unclear, but
may indicate that control of the protein biosynthesis machinery is
important for the oxidative equilibrium of the cell, in agreement
with recent data showing that changes in translational fidelity affect
this balance.48
In conclusion, the recent characterization of the CARA strain
strongly supports the emerging concept that Pol I activity is a key
element for the coordinated synthesis of ribosome components. To
dissect the molecular mechanisms involved, and more specifically
to understand how the level of Pol I transcription impacts on Pol II
transcription will certainly represent a major breakthrough. Another
important issue is to elucidate how Pol I activity influence the level
of the 5S rRNA synthesized by the Pol III. In CARA cells, upon
rapamycin treatment, we observed an attenuated decrease of the level
of this transcript concomitant to the attenuated down regulation
of Pol I transcription.1 Whether this
deregulation of 5S rRNA is transcriptional and/or post‑transcriptional is an
important question that remains to be
addressed.
Finally, a crucial question is to determine whether the central role of Pol
I activity in the control of ribosome
biogenesis has been evolutionarily
conserved. To unravel how human cells
regulate ribosome biogenesis is essential, as exemplified by numerous data
suggesting that altering the protein
synthesis machinery may promote Figure 3. CARA cells are hypersensitive to rapamycin and resistant to H2O2. Wild‑type (WT) or CARA cells
malignant progression (see Ref. 49 for a were harvested either in log‑phase (OD600 = 1, Log) or after the post‑diauxic transition (two days of culture,
review). The possibility that Pol I activity Post‑D). Serial dilutions from the same number of cells were spotted on YPD plates (A), either supplemented
plays in mammalian cells a predominant with rapamycin (0.1 mg/ml) (B) or with H2O2 (3 and 5 mM) (C and D). Growth of WT and CARA colonies
role for the supply of ribosome compo- was analyzed after seven days of incubation at 30˚C.
nents rationalizes the abundant evidence
that Pol I transcription is altered in cancer cells. It may also explain
References
why changes in nucleolar structure are recognized as a reliable 1. Laferté A, Favry E, Sentenac A, Riva M, Carles C, Chédin S. The transcriptional activity
of RNA polymerase I is a key determinant for the level of all ribosome components. Genes
marker of cellular transformation.50 Whether deregulation of Pol I
and Dev 2006; 20:2030‑40.
transcription might be an initiating step in tumorigenesis (see ref. 51
2. Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 1999;
for a discussion of this hypothesis) by promoting increased cellular
24:437‑40.
growth, proliferation, and transformation is thus a critical question 3. Warner JR, Vilardell J, Sohn JH. Economics of ribosome biosynthesis. Cold Spring Harb
that needs to be addressed in the near future.
Symp Quant Biol 2001; 66:567‑74.
14
Cell Cycle
2007; Vol. 6 Issue 1
Pol I and Ribosome Biogenesis
4. Keys DA, Lee BS, Dodd JA, Nguyen TT, Vu L, Fantino E, Burson LM, Nogi Y, Nomura
M. Multiprotein transcription factor UAF interacts with the upstream element of the yeast
RNA polymerase I promoter and forms a stable preinitiation complex. Genes and Dev
1996; 10:887‑903.
5. Lalo D, Steffan JS, Dodd JA, Nomura M. RRN11 encodes the third subunit of the complex
containing Rrn6p and Rrn7p that is essential for the initiation of rDNA transcription by
yeast RNA polymerase I. J Biol Chem 1996; 271:21062‑7.
6. Steffan J, Keys D, Dodd J, Nomura M. The role of TBP in rDNA transcription by RNA
polymerase I in Saccharomyces cerevisiae: TBP is required for upstream activation factor
dependent recruitment of core factor. Genes and Dev 1996; 10:2551‑63.
7. Yamamoto RT, Nogi Y, Dodd JA, Nomura M. RRN3 gene of Saccharomyces cerevisiae
encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. EMBO J 1996; 15:3964‑73.
8. Milkereit P, Tschochner H. A specialized form of RNA polymerase I, essential for initiation
and growth‑dependent regulation of rRNA synthesis, is disrupted during transcription.
EMBO J 1998; 17:3692‑705.
9. Moss T, Stefanovsky VY. At the center of eukaryotic life. Cell 2002; 109:545‑8.
10. Grummt I. Life on a planet of its own: Regulation of RNA polymerase I transcription in the
nucleolus. Genes and Dev 2003; 17:1691‑702.
11. Russell J, Zomerdijk JC. The RNA polymerase I transcription machinery. Biochem Soc
Symp 2006; 203‑16.
12. Miller G, Panov KI, Friedrich JK, Trinkle‑Mulcahy L, Lamond AI, Zomerdijk JC. hRRN3
is essential in the SL1‑mediated recruitment of RNA Polymerase I to rRNA gene promoters.
EMBO J 2001; 20:1373‑82.
13. Mayer C, Zhao J, Yuan X, Grummt I. mTOR‑dependent activation of the transcription factor TIF‑IA links rRNA synthesis to nutrient availability. Genes and Dev 2004; 18:423‑34.
14. Peyroche G, Milkereit P, Bischler N, Tschochner H, Schultz P, Sentenac A, Carles C, Riva
M. The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the
A43 subunit with Rrn3. EMBO J 2000; 19:5473‑82.
15. Ju Q, Warner JR. Ribosome synthesis during the growth cycle of Saccharomyces cerevisiae.
Yeast 1994; 10:151‑7.
16. Gasch AP, Spellman PT, Kao CM, Carmel‑Harel O, Eisen MB, Storz G, Botstein D, Brown
PO. Genomic expression programs in the response of yeast cells to environmental changes.
Mol Biol Cell 2000; 11:4241‑57.
17. Lin YS, Hwang JK, Li WH. Protein complexity, gene duplicability and gene dispensability
in the yeast genome. Gene 2006; In press.
18. Bernstein KA, Gallagher JE, Mitchell BM, Granneman S, Baserga SJ. The small‑subunit
processome is a ribosome assembly intermediate. Eukaryot Cell 2004; 3:1619‑26.
19. Liu PC, Thiele DJ. Novel stress‑responsive genes EMG1 and NOP14 encode conserved, interacting proteins required for 40S ribosome biogenesis. Mol Biol Cell 2001;
12:3644‑57.
20. Van Dyke MW, Nelson LD, Weilbaecher RG, Mehta DV. Stm1p, a G4 quadruplex and
purine motif triplex nucleic acid‑binding protein, interacts with ribosomes and subtelomeric
Y’ DNA in Saccharomyces cerevisiae. J Biol Chem 2004; 279:24323‑33.
21. Phan L, Zhang X, Asano K, Anderson J, Vornlocher HP, Greenberg JR, Qin J, Hinnebusch
AG. Identification of a translation initiation factor 3 (eIF3) core complex, conserved in yeast
and mammals, that interacts with eIF5. Mol Cell Biol 1998; 18:4935‑46.
22. Baum S, Bittins M, Frey S, Seedorf M. Asc1p, a WD40‑domain containing adaptor protein, is required for the interaction of the RNA‑binding protein Scp160p with polysomes.
Biochem J 2004; 380:823‑30.
23. Hohmann S, Thevelein JM. The cell division cycle gene CDC60 encodes cytosolic
leucyl‑tRNA synthetase in Saccharomyces cerevisiae. Gene 1992; 120:43‑9.
24. Miller T, Krogan NJ, Dover J, Erdjument‑Bromage H, Tempst P, Johnston M, Greenblatt
JF, Shilatifard A. COMPASS: A complex of proteins associated with a trithorax‑related SET
domain protein. Proc Natl Acad Sci USA 2001; 98:12902‑7.
25. Roguev A, Schaft D, Shevchenko A, Pijnappel WW, Wilm M, Aasland R, Stewart AF. The
Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone
3 lysine 4. EMBO J 2001; 20:7137‑48.
26. Caspary F, Séraphin B. The yeast U2A’/U2B complex is required for prespliceosome formation. EMBO J 1998; 17:6348‑58.
27. Cheng C, Huang D, Roach PJ. Yeast PIG genes: PIG1 encodes a putative type 1 phosphatase subunit that interacts with the yeast glycogen synthase Gsy2p. Yeast 1997; 13:1‑8.
28. Hassett RF, Yuan DS, Kosman DJ. Spectral and kinetic properties of the Fet3 protein from
Saccharomyces cerevisiae, a multinuclear copper ferroxidase enzyme. J Biol Chem 1998;
273:23274‑82.
29. Shi X, Stoj C, Romeo A, Kosman DJ, Zhu Z. Fre1p Cu2+ reduction and Fet3p Cu1+
oxidation modulate copper toxicity in Saccharomyces cerevisiae. J Biol Chem 2003;
278:50309‑15.
30. Mack D, Nishimura K, Dennehey BK, Arbogast T, Parkinson J, Toh‑e A, Pringle JR, Bender
A, Matsui Y. Identification of the bud emergence gene BEM4 and its interactions with
rho‑type GTPases in Saccharomyces cerevisiae. Mol Cell Biol 1996; 16:4387‑95.
31. Askree SH, Yehuda T, Smolikov S, Gurevich R, Hawk J, Coker C, Krauskopf A, Kupiec M,
McEachern MJ. A genome‑wide screen for Saccharomyces cerevisiae deletion mutants that
affect telomere length. Proc Natl Acad Sci USA 2004; 101:8658‑63.
32. Wu M, Tzagoloff A. Identification and characterization of a new gene (CBP3) required
for the expression of yeast coenzyme QH2‑cytochrome c reductase. J Biol Chem 1989;
264:11122‑30.
www.landesbioscience.com
33. Shi G, Crivellone MD, Edderkaoui B. Identification of functional regions of Cbp3p, an
enzyme‑specific chaperone required for the assembly of ubiquinol‑cytochrome c reductase
in yeast mitochondria. Biochim Biophys Acta 2001; 1506:103‑16.
34. Graack HR, Wittmann‑Liebold B. Mitochondrial ribosomal proteins (MRPs) of yeast.
Biochem J 1998; 329(Pt 3):433‑48.
35. Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size.
Genes and Dev 2004; 18:2491‑505.
36. Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis‑regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.
J Mol Biol 2000; 296:1205‑14.
37. Wade C, Shea KA, Jensen RV, McAlear MA. EBP2 is a member of the yeast RRB regulon, a
transcriptionally coregulated set of genes that are required for ribosome and rRNA biosynthesis. Mol Cell Biol 2001; 21:8638‑50.
38. Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M. Systematic identification of pathways
that couple cell growth and division in yeast. Science 2002; 297:395‑400.
39. Miyoshi K, Shirai C, Mizuta K. Transcription of genes encoding trans‑acting factors
required for rRNA maturation/ribosomal subunit assembly is coordinately regulated with
ribosomal protein genes and involves Rap1 in Saccharomyces cerevisiae. Nucleic Acids Res
2003; 31:1969‑73.
40. Fatica A, Tollervey D. Making ribosomes. Curr Opin Cell Biol 2002; 14:313‑8.
41. Mizuta K, Warner JR. Continued functioning of the secretory pathway is essential for ribosome synthesis. Mol Cell Biol 1994; 14:2493‑502.
42. Zaragoza D, Ghavidel A, Heitman J, Schultz MC. Rapamycin induces the G0 program of
transcriptional repression in yeast by interfering with the TOR signaling pathway. Mol Cell
Biol 1998; 18:4463‑70.
43. Powers T, Walter P. Regulation of ribosome biogenesis by the rapamycin‑sensitive
TOR‑signaling pathway in Saccharomyces cerevisiae. Mol Biol Cell 1999; 10:987‑1000.
44. Li Y, Moir RD, Sethy‑Coraci IK, Warner JR, Willis IM. Repression of ribosome and tRNA
synthesis in secretion‑defective cells is signaled by a novel branch of the cell integrity pathway. Mol Cell Biol 2000; 20:3843‑51.
45. Upadhya R, Lee J, Willis IM. Maf1 is an essential mediator of diverse signals that repress
RNA polymerase III transcription. Mol Cell 2002; 10:1489‑94.
46. Preiss T, Baron‑Benhamou J, Ansorge W, Hentze MW. Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat
Struct Biol 2003; 10:1039‑47.
47. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL,
Lander ES, Young RA. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 2001; 12:323‑37.
48. Konstantinidis TC, Patsoukis N, Georgiou CD, Synetos D. Translational fidelity mutations
in 18S rRNA affect the catalytic activity of ribosomes and the oxidative balance of yeast cells.
Biochemistry 2006; 45:3525‑33.
49. Ruggero D, Pandolfi PP. Does the ribosome translate cancer? Nat Rev Cancer 2003;
3:179‑92.
50. Gani R. The nucleoli of cultured human lymphocytes. I. Nucleolar morphology in relation
to transformation and the DNA cycle. Exp Cell Res 1976; 97:249‑58.
51. Rosenwald IB. Deregulation of protein synthesis as a mechanism of neoplastic transformation. BioEssays 1996; 18:243‑50.
52. Hoang T, Peng WT, Vanrobays E, Krogan N, Hiley S, Beyer AL, Osheim YN, Greenblatt
J, Hughes TR, Lafontaine DL. Esf2p, a U3‑associated factor required for small‑subunit
processome assembly and compaction. Mol Cell Biol 2005; 25:5523‑34.
53. Lafontaine DL, Tollervey D. The function and synthesis of ribosomes. Nat Rev Mol Cell
Biol 2001; 2:514‑20.
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